AMBER Archive (2004)

Subject: RE: AMBER: VDWAALS error during minimisation

From: Ross Walker (
Date: Thu Sep 16 2004 - 10:20:34 CDT

Dear Anita,

The xxxxx means that the value is TOO BIG to fit in the number of spaces
specified for the output file. This means that you most probably have two
atoms that are very close together. If you did MD here you would probably
find that your system would quickly 'blow up' due to excessive initial
forces on these atoms. The situation is not as bad with minimisation however
as the steepest descent algorithm will quickly relax the initial strains.
You may find that your minimised structure is acceptable. Your best bet is
to create a pdb of the final structure and see if it is reasonable.
Hopefully if the VDW's were not too big (I.e were not approximated to
infinity) then the minimiser will probably have done something sensible. If
the VDW were so large (typically if two atoms are on top of each other) then
the behaviour of the minimiser will have been undefined. Best option is to
look at the final structure and see if it is what you expect.

Note, you can check the structure in xleap before you save the prmtop and
inpcrd files and it should list all close contacts. Also take a look at the
first minimisation steps, the output lists the atom which had the largest
force on it. This will probably be the atom with the larges VDW energy. Most
likely it is due to the ligand you docked in.

So, check the final structure before doing MD. Also run a few hundred steps
of MD, dumping every step so that you can visualise the initial MD behaviour
to see if it is reasonable.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |


> -----Original Message-----
> From:
> [] On Behalf Of anita pachaimuthu
> Sent: 16 September 2004 07:43
> To:
> Subject: AMBER: VDWAALS error during minimisation
> Hi,
> The min.out file during minimsation has xxxxx in VDWAALS for
> the first 14 Nstep steps.Can somebody help me find the reason
> for the error and can i ignore this error and proceed to equilibrate.
> The input file to minimisation is a docked file where i
> allowed some bonds to roatate ,could this be the one causing
> the problem.
> Thanking You,
> Anita

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to